I had exactly the same issue, every week for like 2 months - exercise 12/13 (i.e. circuit bashing). I'd always flare too early so the plane would bump down - it is always later than you think.
My instructor was very patient but ultimately it is something you learn through practice. The best advice was perhaps to plan to fly down the runway - no need to execute a short field landing during the first 20 feet. If you plan to fly down the runway and slowly descend then you get a feel for it. Then next time you'll find yourself eating-up less of the runway etc. Worst case, you go around - no harm done!